Variant report

Variant	rs3899004
Chromosome Location	chr4:79409043-79409044
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10001798	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10001918	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10018235	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10026662	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1006079	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1027444	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1027447	0.80[EUR][1000 genomes]
rs1027449	0.80[EUR][1000 genomes]
rs11098196	0.96[ASN][1000 genomes]
rs11730871	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13106736	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13107007	0.82[EUR][1000 genomes]
rs13118276	0.80[EUR][1000 genomes]
rs13132231	0.82[EUR][1000 genomes]
rs13141571	0.80[EUR][1000 genomes]
rs13143325	0.80[EUR][1000 genomes]
rs1484331	0.83[EUR][1000 genomes]
rs1484342	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1484343	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1496581	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1496582	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1496583	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1496584	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1496585	0.83[EUR][1000 genomes]
rs1496586	0.83[EUR][1000 genomes]
rs1496587	0.83[EUR][1000 genomes]
rs1496607	0.80[EUR][1000 genomes]
rs17003266	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17003289	0.83[EUR][1000 genomes]
rs17003293	0.80[EUR][1000 genomes]
rs17003294	0.80[EUR][1000 genomes]
rs2035511	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2054721	0.83[EUR][1000 genomes]
rs2627648	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2627649	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2627650	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2627651	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2627653	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2627654	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2627655	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2627656	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2645143	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2645144	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2645145	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2645146	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2645147	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2645148	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2645149	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28361383	0.80[EUR][1000 genomes]
rs28449192	0.80[EUR][1000 genomes]
rs28473345	0.80[EUR][1000 genomes]
rs28488385	0.80[EUR][1000 genomes]
rs28522970	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28545653	0.80[EUR][1000 genomes]
rs28566963	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28570979	0.80[EUR][1000 genomes]
rs28651081	0.80[EUR][1000 genomes]
rs2867068	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2867070	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2867447	0.82[EUR][1000 genomes]
rs2867450	0.81[EUR][1000 genomes]
rs2867451	0.81[EUR][1000 genomes]
rs28704649	0.80[EUR][1000 genomes]
rs28721400	0.80[EUR][1000 genomes]
rs28725393	0.80[EUR][1000 genomes]
rs28739412	0.80[EUR][1000 genomes]
rs2903470	0.83[EUR][1000 genomes]
rs34840208	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35150477	0.80[EUR][1000 genomes]
rs35520641	0.80[EUR][1000 genomes]
rs36095733	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3749488	0.80[EUR][1000 genomes]
rs3762844	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3792608	0.80[EUR][1000 genomes]
rs4975065	0.83[EUR][1000 genomes]
rs4975067	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4975128	0.96[ASN][1000 genomes]
rs59249633	0.80[EUR][1000 genomes]
rs59857077	0.80[EUR][1000 genomes]
rs60285643	0.81[EUR][1000 genomes]
rs60520656	0.80[EUR][1000 genomes]
rs62310269	0.80[EUR][1000 genomes]
rs62310270	0.80[EUR][1000 genomes]
rs62310273	0.80[EUR][1000 genomes]
rs62310274	0.80[EUR][1000 genomes]
rs62310275	0.80[EUR][1000 genomes]
rs67201837	0.85[AMR][1000 genomes]
rs67217470	0.81[EUR][1000 genomes]
rs67993554	0.80[EUR][1000 genomes]
rs6816851	0.83[EUR][1000 genomes]
rs753751	0.83[EUR][1000 genomes]
rs753752	0.83[EUR][1000 genomes]
rs7674053	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7699000	0.83[EUR][1000 genomes]
rs924149	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs949507	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs959539	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79343200-79431800	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr4:79363200-79409800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:79363400-79455200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr4:79363800-79464200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:79376200-79411600	Weak transcription	Fetal Stomach	stomach
6	chr4:79378600-79455800	Weak transcription	Right Ventricle	heart
7	chr4:79385000-79467400	Weak transcription	Fetal Brain Male	brain
8	chr4:79393800-79467200	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr4:79396800-79410000	Weak transcription	Pancreas	Pancrea
10	chr4:79398000-79409400	Weak transcription	Fetal Lung	lung
11	chr4:79399200-79409800	Weak transcription	Aorta	Aorta
12	chr4:79399200-79410000	Weak transcription	Esophagus	oesophagus
13	chr4:79399400-79409800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr4:79401000-79467200	Weak transcription	Psoas Muscle	Psoas
15	chr4:79402000-79427600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr4:79402400-79409600	Weak transcription	HSMMtube	muscle
17	chr4:79403000-79420200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr4:79403200-79428000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr4:79403200-79449800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr4:79403600-79409800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr4:79403800-79409800	Weak transcription	Fetal Kidney	kidney
22	chr4:79403800-79411000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr4:79403800-79428000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr4:79404000-79409800	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr4:79404000-79427200	Weak transcription	Fetal Intestine Small	intestine
26	chr4:79404200-79450200	Weak transcription	HMEC	breast
27	chr4:79404400-79431800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr4:79404600-79409800	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr4:79405000-79410000	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr4:79406000-79409800	Weak transcription	HepG2	liver
31	chr4:79406200-79416400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr4:79406400-79409600	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr4:79407200-79410000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr4:79407400-79415600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr4:79407400-79417400	Weak transcription	Fetal Intestine Large	intestine
36	chr4:79407600-79409600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr4:79407600-79409600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr4:79408000-79411200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr4:79408200-79409600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr4:79408200-79411200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr4:79408600-79435000	Weak transcription	Fetal Heart	heart

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